Gene expression profiling has the potential to revolutionize current approaches to cancer classification and diagnosis. Recent cDNA microarray analyses of moles, primary and metastatic melanomas performed in our laboratory have identified a number of genes whose expression level can be used to distinguish between known landmarks in the tumor progression cascade of melanoma. These studies have suggested the utility of gene expression profiling to develop a novel molecular classification of melanocytic neoplasms. In this application, we propose to extend these observations by developing a molecular classification of melanoma using gene expression profiling. We will also assess the utility of immunohistochemical analysis to develop molecular diagnostic and prognostic markers for melanoma. Our aims are: Aim 1: To classify the molecular subtypes of primary melanoma by gene expression profiling of a large cohort of melanoma patients. Aim 2: To assess the utility of immunohistochemical analysis of multiple molecular markers to differentiate primary melanomas from benign nevi. We will examine the protein expression of eight markers identified in our cDNA microarray analysis as being differentially expressed in melanomas when compared with nevi in a test set of 350 primary melanomas and 150 nevi, and a validation set of 75 cases of primary melanoma arising in a nevus. Aim 3: To assess the utility of immunohistochemical analysis of multiple molecular markers for their ability to predict the prognosis associated with melanoma. We will examine whether eight molecular markers identified in our cDNA microarray analysis as being differentially expressed in metastatic melanomas can predict melanoma prognosis when analyzed at the protein level. We will use immunohistochemical analysis to quantitate expression of these eight markers in a cohort of 353 primary melanomas with defined histology and follow up. Overall, these studies should more precisely characterize the molecular basis of melanoma heterogeneity, and identify novel diagnostic and prognostic markers for primary melanoma.